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Satrio Wibowo

dblp:425/2646 · DBLP profile ↗
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1ranked-venue papers
0as first author
1since 2021 · last 2024
0000-0002-8892-3808ORCID · reported

Domains — the database's venue-derived domains; a paper can count in several

Applied, interdisciplinary, general and emerging computing · 1 · 1 since 2021

Expertise — from the expertise taxonomy: the topics of the expert's papers under the CCF categories. A weight counts papers with recency: 1 for a paper about the topic, 0.3 when the topic is its context, halved every five years.

Interdisciplinary, comprehensive, and emerging computing
1 paper
Bioinformatics and computational biology · 100%

Topics — the 2 heaviest of 2, each with the papers that count most for it

TopicWeightPapersLastEvidence papers
Bioinformatics and computational biology › sequence analysis
nanopore sequencing
0.812024
Icarust, a real-time simulator for Oxford Nanopore adaptive sampling · Bioinform. 2024
Bioinformatics and computational biology
sequencing simulation
0.812024
Icarust, a real-time simulator for Oxford Nanopore adaptive sampling · Bioinform. 2024

Methods — techniques the papers use, named apart from their topics

rust · 0.8docker · 0.8
YearPublicationVenuePosition
2024 Icarust, a real-time simulator for Oxford Nanopore adaptive sampling
abstract
MOTIVATION: Oxford Nanopore Technologies (ONT) sequencers enable real-time generation of sequence data, which allows for concurrent analysis during a run. Adaptive sampling leverages this real-time capability in extremis, rejecting or accepting reads for sequencing based on assessment of the sequence from the start of each read. This functionality is provided by ONT's software, MinKNOW (Oxford Nanopore Technologies). Designing and developing software to take advantage of adaptive sampling can be costly in terms of sequencing consumables, using precious samples and preparing sequencing libraries. MinKNOW addresses this in part by allowing the replay of previously sequenced runs for testing. However, as we show, the sequencing output only partially changes in response to adaptive sampling instructions. Here we present Icarust, a tool enabling more accurate approximations of sequencing runs. Icarust recreates all the required endpoints of MinKNOW to perform adaptive sampling and writes output compatible with current base-callers and analysis pipelines. Icarust serves nanopore signal simulating a MinION or PromethION flow cell experiment from any reference genome using either R9 or R10 pore models. We show that simulating sequencing runs with Icarust provides a realistic testing and development environment for software exploiting the real-time nature of Nanopore sequencing. AVAILABILITY AND IMPLEMENTATION: All code is open source and freely available here-https://github.com/LooseLab/Icarust. Icarust is implemented in Rust, with a docker container also available. The data underlying this article will be shared on reasonable request to the corresponding author.
Rory Munro, Satrio Wibowo, Alexander Payne, Matthew Loose
Bioinform.2